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    <title>Identification - Adduct search</title>
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<h1>Adduct Search</h1>

<h2>Description</h2>

<h4>Definition of an adduct ion</h4>

<p>
    An ion formed by interaction of two species, usually an ion and a molecule, and often within the ion source, to form
    an ion containing all the constituent atoms of one species as well as an additional atom or atoms.
</p>

<p>
    This method identifies common adducts (selected by the user) in a single peak list. The adducts are identified by
    two conditions:
</p>

<ul>
    <li>the retention time of the original ion and the adduct ion should be same, and</li>
    <li>the mass difference between the original ion and the adduct must be equal to one of the adducts selected by the
        user
    </li>

</ul>

<p>
    MZmine has a built-in list of common adducts and their masses. The user can add custom adducts either individually
    or by loading them from a file. Once custom adducts have been added or loaded they will become part of the
    application configuration and don't have to be added/loaded again.
</p>

<p>
    The following figure shows a spectrum with a phosphate adduct ion.<br/>
    <img src="phosphateAdduct.png">
</p>

<p>
    The following figure shows a peak list after identifying two "Deuterium" adducts.<br/>
    <img src="peakList.png">
</p>

<h4>Method parameters</h4>
<dl>
    <dt>RT tolerance</dt>
    <dd>Maximum permissible difference in retention time to set a relationship between peaks</dd>

    <dt>Adducts</dt>
    <dd>List of adducts, each refers a specific m/z difference between related peaks</dd>

    <dt>m/z tolerance</dt>
    <dd>Tolerance value of the m/z difference between peaks</dd>

    <dt>Max adduct peak height</dt>
    <dd>Maximum height of the recognized adduct peak, relative to the main peak</dd>
</dl>

<h4>Adduct choices</h4>

<p>The figure below shows the Adduct Search parameters dialog. Beside the list of adducts are four buttons that function
    as follows:
</p>

<dl>
    <dt>All</dt>
    <dd>Selects all of the check-boxes in the list of adducts.</dd>
    <dt>Clear</dt>
    <dd>Clears the check-boxes in the list of adducts.</dd>
    <dt>Add...</dt>
    <dd>Allows the user to specify an individual custom adduct. A dialog is displayed in which the user can enter the
        name and mass difference of the new adduct.
    </dd>
    <dt>Import...</dt>
    <dd>Loads custom adducts from a comma-separated values (CSV) file. The file should be formatted with one adduct
        defined per line, with each line having the adduct's name and mass difference values separated by a comma.
    </dd>
    <dt>Export...</dt>
    <dd>Saves the adducts to a comma-separated values (CSV) file.</dd>
    <dt>Reset</dt>
    <dd>Restores the list of adducts to the original default set.</dd>
</dl>

<img src="parameters.png">

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